Table 2.
Transcriptional changes in genes involved in epigenetic mechanisms as obtained by mRNA-Seq on 7 and 14 dai giant cells (versus control vascular root cells) and 7 dai galls (versus control root tips; data extracted from Kyndt et al., 2012a )
| Log2FC gall 7 dai vs control root tips | Log2FC giant cell 7 dai vs control root cells | Log2FC giant cell 14 dai vs control root cells | Annotation | |
|---|---|---|---|---|
| Post-transcriptional gene silencing | ||||
| LOC_Os01g16870 | 0.02 | 1.98 | 0.73 | Argonaute |
| LOC_Os01g16860 | 1.58 | 1.37 | NE | AGO4-2 |
| LOC_Os10g34430 | 5.35 | 7.03 | 0.01 | Dicer |
| LOC_Os04g43050 | 2.45 | 1.90 | 0.76 | Dicer |
| LOC_Os04g39160 | 2.78 | 4.59 | 2.04 | RNA-dependent RNA polymerase |
| LOC_Os01g34350 | 2.19 | 0.54 | −6.89 | RNA-dependent RNA polymerase |
| LOC_Os02g58490 | −0.26 | 4.70 | 3.79 | PINHEAD |
| LOC_Os04g47870 | 1.91 | 2.45 | 0.35 | PINHEAD |
| Histone modification | ||||
| LOC_Os01g56540 | 1.00 | 3.99 | NE | Histone-lysine N-methyltransferase SUVR3 |
| LOC_Os01g59620 | 2.16 | 4.25 | 4.25 | Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH1 |
| LOC_Os07g25450 | −0.09 | 5.87 | −0.15 | Histone-lysine N-methyltransferase |
| LOC_Os08g10470 | 0.03 | 7.56 | 4.91 | Histone-lysine N-methyltransferase ASHR2 |
| LOC_Os12g32374 | −0.88 | 4.89 | 2.20 | Histone deacetylase 6 |
| LOC_Os05g36920 | 0.88 | 5.53 | −3.11 | Histone deacetylase |
| LOC_Os10g28040 | −0.45 | 5.58 | −2.98 | Histone acetyltransferase GCN5 |
| LOC_Os06g38470 | 0.97 | 3.19 | 1.10 | Histone deacetylase HDAC1 |
NE, not expressed.